Defines of pin user labels are found in the file atmel_start_pins.h. These user labels match what is configured in the PINMUX CONFIGURATOR.
For example, PA2 is given a user label my_pin, which can be seen configured as specified in the driver_init.c file:
void system_init() { mcu_init(); /* PORT setting on PA2 */ // Set pin direction to output my_pin_set_dir(PORT_DIR_OUT); my_pin_set_level( // <y> Initial level // <id> pad_initial_level // <false"> Low // <true"> High false); CLKCTRL_init(); USART_0_initialization(); CPUINT_init(); SLPCTRL_init(); BOD_init(); }